Estimate Death Fraction
for(i in 1:length(allfiles)) {
f <- allfiles[i]
parf <- allparfiles[i]
fname <- paste0(path,f)
parfname <- paste0(path,parf)
statename <- gsub("\\.csv","",f)
# death fraction
daterange <- read_csv(fname) %>% pull(date) %>% range() %>% as.Date()
dates <- seq(daterange[1],daterange[2],1)
t <- seq_along(dates)
statepars <- readRDS(parfname)
frac_hosp <- statepars['frac_hosp','X1'] # fraction hospitalized
# CFR <- ma(dat.deaths) / ma(dat.cases)
# death_fraction <- CFR * frac_hosp
min_frac_dead <- statepars['min_frac_dead','X1'] # minimum death fraction
max_frac_dead <- statepars['max_frac_dead','X1'] # maximum death fraction
log_half_dead <- statepars['log_half_dead','X1'] # time to 1/2 difference between min and max
fatality <- read.csv(fname) %>%
select(date,variable,mean_value) %>%
mutate(date = as.Date(date)) %>%
filter(variable %in% c("actual_daily_deaths","actual_daily_cases")) %>%
pivot_wider(names_from = variable, values_from = mean_value)
fatality <- fatality %>%
add_row(date = dates[!(dates %in% fatality$date)]) %>%
mutate(crudeCFR = actual_daily_deaths/actual_daily_cases,
maCFR = ma(actual_daily_deaths)/ma(actual_daily_cases),
frac_hosp = frac_hosp,
maHFR = maCFR * 1/frac_hosp,
estHFR = max_frac_dead - (max_frac_dead - min_frac_dead) * (t / (t + log_half_dead)))
fatality %>%
ggplot(aes(x = date, y = maHFR)) +
geom_line(color = "blue") +
geom_line(aes(x = date, y = maCFR), color = "red") +
ylab("Hosp. FR from data (blue), CFR from data (red)") +
geom_line(aes(x = date, y = estHFR)) +
geom_hline(yintercept=min_frac_dead, linetype="dashed") +
geom_hline(yintercept=max_frac_dead, linetype="dashed") +
geom_hline(yintercept=(max_frac_dead+min_frac_dead)/2,linetype="dashed") +
geom_vline(xintercept=daterange[1]+log_half_dead, linetype="dashed") +
ggtitle(statename) +
xlab("") +
ylim(0,1) +
theme(legend.position = "none") -> g_deathfrac
print(g_deathfrac)
}
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## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 65 rows containing missing values (geom_path).
## Warning: Removed 65 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 49 rows containing missing values (geom_path).
## Warning: Removed 49 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 48 rows containing missing values (geom_path).
## Warning: Removed 48 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 55 rows containing missing values (geom_path).
## Warning: Removed 55 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 50 rows containing missing values (geom_path).
## Warning: Removed 50 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 45 rows containing missing values (geom_path).
## Warning: Removed 45 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 54 rows containing missing values (geom_path).
## Warning: Removed 54 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 54 rows containing missing values (geom_path).
## Warning: Removed 54 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 73 rows containing missing values (geom_path).
## Warning: Removed 73 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 48 rows containing missing values (geom_path).
## Warning: Removed 48 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 54 rows containing missing values (geom_path).
## Warning: Removed 54 rows containing missing values (geom_path).
## Parsed with column specification:
## cols(
## location = col_character(),
## sim_type = col_character(),
## period = col_character(),
## date = col_date(format = ""),
## variable = col_character(),
## lower_80 = col_double(),
## lower_90 = col_double(),
## lower_95 = col_double(),
## mean_value = col_double(),
## median_value = col_double(),
## upper_80 = col_double(),
## upper_90 = col_double(),
## upper_95 = col_double()
## )

## Warning: Removed 57 rows containing missing values (geom_path).
## Warning: Removed 57 rows containing missing values (geom_path).
